Package: Seurat
Version: 4.0.5
Date: 2021-10-04
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Authors@R: c(
  person(given = "Andrew", family = "Butler", email = "abutler@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-3608-0463")),
  person(given = "Saket", family = "Choudhary", email = "schoudhary@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5202-7633")),
  person(given = "Charlotte", family = "Darby", email = "cdarby@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-2195-5300")),
  person(given = "Jeff", family = "Farrell", email = "jfarrell@g.harvard.edu", role = "ctb"),
  person(given = "Christoph", family = "Hafemeister", email = "chafemeister@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-6365-8254")),
  person(given = "Yuhan", family = "Hao", email = "yhao@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-1810-0822")),
  person(given = "Paul", family = "Hoffman", email = "seurat@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7693-8957")),
  person(given = "Jaison", family = "Jain", email = "jjain@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")),
  person(given = "Efthymia", family = "Papalexi", email = "epapalexi@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5898-694X")),
  person(given = "Patrick", family = "Roelli", email = "proelli@nygenome.org", role = "ctb"),
  person(given = "Rahul", family = "Satija", email = "rsatija@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-9448-8833")),
  person(given = "Karthik", family = "Shekhar", email = "kshekhar@berkeley.edu", role = "ctb"),
  person(given = "Avi", family = "Srivastava", email = "asrivastava@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-9798-2079")),
  person(given = "Tim", family = "Stuart", email = "tstuart@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-3044-0897")),
  person(given = "Kristof", family = "Torkenczy", email = "", role = "ctb", comment = c(ORCID = "0000-0002-4869-7957")),
  person(given = "Shiwei", family = "Zheng", email = "szheng@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-6682-6743")),
  person("Satija Lab and Collaborators", role = "fnd")
  )
URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat
BugReports: https://github.com/satijalab/seurat/issues
Depends:
    R (>= 4.0.0),
    methods
Imports:
    cluster,
    cowplot,
    fitdistrplus,
    future,
    future.apply,
    ggplot2 (>= 3.3.0),
    ggrepel,
    ggridges,
    graphics,
    grDevices,
    grid,
    httr,
    ica,
    igraph,
    irlba,
    jsonlite,
    KernSmooth,
    leiden (>= 0.3.1),
    lmtest,
    MASS,
    Matrix (>= 1.2-14),
    matrixStats,
    miniUI,
    patchwork,
    pbapply,
    plotly (>= 4.9.0),
    png,
    RANN,
    RColorBrewer,
    Rcpp (>= 1.0.7),
    RcppAnnoy (>= 0.0.18),
    reticulate,
    rlang,
    ROCR,
    Rtsne,
    scales,
    scattermore (>= 0.7),
    sctransform (>= 0.3.2),
    SeuratObject (>= 4.0.2),
    shiny,
    spatstat.core,
    spatstat.geom,
    stats,
    tibble,
    tools,
    utils,
    uwot (>= 0.1.9)
LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress
License: GPL-3 | file LICENSE
LazyData: true
Collate:
    'RcppExports.R'
    'reexports.R'
    'generics.R'
    'clustering.R'
    'visualization.R'
    'convenience.R'
    'data.R'
    'differential_expression.R'
    'dimensional_reduction.R'
    'integration.R'
    'mixscape.R'
    'objects.R'
    'preprocessing.R'
    'tree.R'
    'utilities.R'
    'zzz.R'
RoxygenNote: 7.1.1
Encoding: UTF-8
Suggests:
    ape,
    rsvd,
    testthat,
    hdf5r,
    S4Vectors,
    SummarizedExperiment,
    SingleCellExperiment,
    MAST,
    DESeq2,
    BiocGenerics,
    GenomicRanges,
    GenomeInfoDb,
    IRanges,
    rtracklayer,
    Rfast2,
    monocle,
    Biobase,
    VGAM,
    limma,
    metap,
    enrichR,
    mixtools